nebbiolo1 Summary
[top]
| Package: ClustAll |
| Version: 0.99.5 |
| RVersion: 4.4
|
| BiocVersion: 3.19
|
| BuildCommand: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ClustAll |
| BuildTime: 3 minutes 58.17 seconds |
| CheckCommand: BiocCheckGitClone('ClustAll') && /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3253/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3253/7517e9e4d9bf7521bfc8eb41840c94937f81b0db/ClustAll.install-out.txt ClustAll_0.99.5.tar.gz && BiocCheck('ClustAll_0.99.5.tar.gz', `new-package`=TRUE) |
| CheckTime: 5 minutes 25.29 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 2758.14 KiB |
| BuildID:: ClustAll_20240207074642 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: ClustAll. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ClustAll/DESCRIPTION ... OK
* preparing ClustAll:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a data/datalist file should be added
* building ClustAll_0.99.5.tar.gz
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('ClustAll')
===============================
BiocCheckVersion: 1.39.23
BiocVersion: 3.19
Package: ClustAll
PackageVersion: 0.99.5
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3253/7517e9e4d9bf7521bfc8eb41840c94937f81b0db/ClustAll
platform: unix
isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* NOTE: (Optional) CITATION file not found. Only include a CITATION
file if there is a preprint or publication for this Bioconductor
package. Note that Bioconductor packages are not required to have
a CITATION file but it is useful both for users and for tracking
Bioconductor project-wide metrics. When including a CITATION
file, add the publication using the 'doi' argument of
'bibentry()'.
BiocCheck results
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3253/7517e9e4d9bf7521bfc8eb41840c94937f81b0db/ClustAll.Rcheck
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file ClustAll/DESCRIPTION ... OK
* checking extension type ... Package
* this is package ClustAll version 0.99.5
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ClustAll can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking build directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [20s/20s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of data directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [23s/131s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
createClustAll 5.019 0.088 5.107
plotJACCARD 1.262 0.061 13.209
showJaccardDistances 0.854 0.035 13.434
showSummaryClusters 0.817 0.007 13.382
plotSANKEY 0.527 0.044 12.445
cluster2data 0.537 0.024 12.466
runClustAll 0.449 0.046 12.424
isProcessed 0.485 0.009 12.381
validateStratification 0.480 0.014 12.355
resStratification 0.480 0.006 12.375
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running runTests.R [27s/59s]
Running test_CreateClustAll.R [6s/6s]
[33s/65s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [3s/3s] OK
* DONE
Status: OK
===============================
BiocCheck('ClustAll_0.99.5.tar.gz')
===============================
BiocCheckVersion: 1.39.23
BiocVersion: 3.19
Package: ClustAll
PackageVersion: 0.99.5
sourceDir: /tmp/RtmpfjrUi7/file3c6dd8116fc8c1/ClustAll
installDir: /tmp/RtmpfjrUi7/file3c6dd843558eeb
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3253/7517e9e4d9bf7521bfc8eb41840c94937f81b0db/ClustAll.BiocCheck
platform: unix
isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.2.0 to 4.4.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* NOTE: Provide 'URL', 'BugReports', 'Date' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (5%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of ClustAll...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 6 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
Registered S3 method overwritten by 'rmutil':
method from
print.response httr
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 127 lines (4%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 556 lines
(20%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
BiocCheck results
0 ERRORS | 1 WARNINGS | 8 NOTES
See the ClustAll.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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merida1 Summary
[top]
| Package: ClustAll |
| Version: 0.99.5 |
| RVersion: 4.4
|
| BiocVersion: 3.19
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ClustAll |
| BuildTime: 9 minutes 52.71 seconds |
| CheckCommand: BiocCheckGitClone('ClustAll') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3253/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3253/7517e9e4d9bf7521bfc8eb41840c94937f81b0db/ClustAll.install-out.txt ClustAll_0.99.5.tar.gz && BiocCheck('ClustAll_0.99.5.tar.gz', `new-package`=TRUE) |
| CheckTime: 14 minutes 48.52 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh ClustAll_0.99.5.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 1 minutes 0.43 seconds |
| PackageFileSize: 2785.22 KiB |
| BuildID:: ClustAll_20240207074642 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: ClustAll. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.WARNING: check time exceeded 10 min. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ClustAll/DESCRIPTION ... OK
* preparing ClustAll:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a data/datalist file should be added
* building ClustAll_0.99.5.tar.gz
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('ClustAll')
===============================
BiocCheckVersion: 1.39.23
BiocVersion: 3.19
Package: ClustAll
PackageVersion: 0.99.5
sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3253/7517e9e4d9bf7521bfc8eb41840c94937f81b0db/ClustAll
platform: unix
isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* NOTE: (Optional) CITATION file not found. Only include a CITATION
file if there is a preprint or publication for this Bioconductor
package. Note that Bioconductor packages are not required to have
a CITATION file but it is useful both for users and for tracking
Bioconductor project-wide metrics. When including a CITATION
file, add the publication using the 'doi' argument of
'bibentry()'.
BiocCheck results
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /Users/pkgbuild/packagebuilder/workers/jobs/3253/7517e9e4d9bf7521bfc8eb41840c94937f81b0db/ClustAll.Rcheck
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option --no-vignettes
* checking for file ClustAll/DESCRIPTION ... OK
* checking extension type ... Package
* this is package ClustAll version 0.99.5
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ClustAll can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking build directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [14s/18s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/18s] OK
* checking whether the package can be unloaded cleanly ... [13s/16s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/16s] OK
* checking whether the namespace can be unloaded cleanly ... [14s/16s] OK
* checking loading without being on the library search path ... [15s/16s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [49s/55s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of data directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [51s/366s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
createClustAll 12.231 0.292 14.409
plotJACCARD 3.218 0.119 41.371
showJaccardDistances 2.005 0.100 36.764
showSummaryClusters 1.998 0.100 36.818
plotSANKEY 1.314 0.118 37.871
cluster2data 1.255 0.129 33.893
resStratification 1.061 0.081 34.287
validateStratification 1.055 0.076 32.846
runClustAll 1.048 0.078 35.356
isProcessed 1.042 0.080 35.218
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running runTests.R [52s/151s]
Running test_CreateClustAll.R [14s/15s]
[66s/166s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [12s/13s] OK
* DONE
Status: OK
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('ClustAll_0.99.5.tar.gz')
===============================
BiocCheckVersion: 1.39.23
BiocVersion: 3.19
Package: ClustAll
PackageVersion: 0.99.5
sourceDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//Rtmpty6Fnc/file1290e2984018e/ClustAll
installDir: /var/folders/97/7zyjn3nj10x926_ht39w_4lm0000gt/T//Rtmpty6Fnc/file1290e2fc99eb0
BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3253/7517e9e4d9bf7521bfc8eb41840c94937f81b0db/ClustAll.BiocCheck
platform: unix
isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.2.0 to 4.4.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* NOTE: Provide 'URL', 'BugReports', 'Date' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (5%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of ClustAll...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 6 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
Registered S3 method overwritten by 'rmutil':
method from
print.response httr
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 127 lines (4%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 556 lines
(20%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
BiocCheck results
0 ERRORS | 1 WARNINGS | 8 NOTES
See the ClustAll.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir ClustAll_0.99.5.tar.gz'
>>>>>>>
* installing *source* package ClustAll ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ClustAll)